Bats buzzed and hissed overhead. The air was hot and thick, tinged with sulfur. Through a corridor below came the sounds of splashing and low murmuring voices.

Cenote Dzitnup, an immense vaulted cavern in the middle of the Yucatán Peninsula, is a strange and otherworldly tourist trap, filled with deep, clear water, flanked with roots, vines and giant stalactites pointing down over an inky abyss. Buses stop there to unload beachgoers from Cancún. German tourists strip naked to put on Speedos before leaping in for a swim. Aboveground, girls work snack stands, and little boys beg to guard your car in the parking lot.

But Cenote Dzitnup is worth the stop. Found just southwest of the town of Valladolid on the way to the Maya ruins at Chichén Itzá, it is an archetype of the unique karst (porous limestone) geology ubiquitous on the Yucatán Peninsula, where water-filled sinkholes called cenotes were literal wellsprings of a civilization.

Trim the jungle down to its roots, scrape away 10,000 years of sediment and mud, and the northern Yucatán is a billion-hole brick of porous stone, flat as a tortilla with hardly a lake in sight. Rivers are practically nonexistent. The area’s odd geology — a subterranean universe of caverns, karst tunnels and cenotes, some hundreds of feet deep — has created a landscape found at few other places on the planet.

“Cenotes are to the Yucatán Peninsula what the Alps are to Switzerland,” said Sam Meacham, director of Centro Investigador del Sistema Acuífero de Quintana Roo, or Cindaq, a nonprofit scientific and educational organization based in Playa del Carmen. “Similar features exist in other parts of the world; however, not in the abundance or natural beauty that we have here.”

Mr. Meacham, a cave diver and researcher originally from Austin, Tex., has explored the aquatic inner workings of the Yucatán since 1995, mapping long underwater caverns and studying the effects of development and pollution on the Yucatán’s vast subterranean watershed. He stands in a long line of explorers who have sought perspective on the region’s human and natural history through the lens of its watery underworld.

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Chichén Itzá, the Maya city now in ruins, was built near three cenotes, or water-filled sinkholes, which provided drinking water for its residents.Credit
Adriana Zehbrauskas for The New York Times

For thousands of years, as natural wells of ever-replenishing fresh water, cenotes (pronounced say-NO-tays) nurtured human life, and the area’s ancient cities — Cobá, Zací, Mayapán, Chichén Itzá — were built on their flanks. An advanced Mesoamerican civilization of temples, pyramids, ball courts and paved roads sprouted and grew not near a seaport or on a riverway, but deep inland at jungle oases.

Cenotes, which may be enclosed caverns like Cenote Dzitnup or steep-sided open pits, became sacred places to the Maya. Food, valued objects and sacrificed bodies were dropped in as offerings to gods.

Archaeological dredging over the past 100 years has cleaned out large and significant cenotes, netting human remains, gold, jade and innumerable clues to a civilization long faded.

But explorers like Mr. Meacham can today still dive down to document skulls, pots and artifacts in the untouched cenotes that dot the hinterlands by the thousands, making a record of the discoveries for archaeologists to follow.

Travelers to the Yucatán snoop and swim in dozens of managed cenotes, snorkeling or spelunking alone or with guides all over the peninsula. Area maps show cenotes as prominent geographical features.

Parks near the ocean in the vicinity of Playa del Carmen and Tulum have cenotes open for swimming, as tourists and locals take cooling dips together in pools of deep spring water.

In late November, as the Yucatán experienced an unusual spell of cool weather, I boarded a second-class bus in downtown Cancún to begin a trip inland and underground, a half-dozen cenotes on my itinerary.

Valladolid, a colonial city of 40,000 that sits over underground rivers and hollow caverns, would serve as my base for daylong adventures to the cenote sites near town.

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The Convent of San Bernardino de Siena a 16th-century Spanish monastery, was built atop a cenote.Credit
Adriana Zehbrauskas for The New York Times

Eighty-nine slimy steps led down to the aquamarine edge of Cenote Zací, a dank crater five blocks from my hotel in Valladolid. The vine-draped pit — my first stop on the cenote trail — was open to the sun and filled with birds.

Before the Spanish founded Valladolid in the mid-1500’s, the Maya city of Zací flourished on the rim of its namesake cenote. Today, Cenote Zací is operated as a park, and 15 pesos (about $1.35 at 11 pesos to the dollar) at the ticket booth grants entrance to a corridor in the limestone outcrop.

Walking in, I paused to let my pupils adjust to the dim light. The path snaked through a cave ahead before dropping back to an amphitheater of sun.

Diving in the deep pool, where blind fish are rumored to live, was my No. 1 objective at Zací. However, a recently installed sign — “Se Prohibe Nadar /No Swimming /Danger” — dissuaded me from doing much more than dipping a toe.

I sat on a bench of limestone masonry instead, working to imagine the Maya community that had lived on the cenote’s rim. As in other settlements in the region, the deep freshwater sinkhole — crawling with bugs, caked with bird droppings and guano, dank, gritty, grimy, sticky, slimy, steamy and wet — was the origin of a community that thrived for hundreds of years.

Even Chichén Itzá — the famous Maya metropolis of pyramids and temples, which I visited the next day — rose from hardscrabble jungle at the edge of three cenotes. The cenotes were the foundation of the city’s infrastructure, wells that sated its thousands of citizens. Sacred Cenote, a round open pit of vines and stratified stone, is connected to Chichén Itzá’s city center via an ancient paved road.

The Yucatán’s first European colonizers depended on cenotes as well, and a model example is found in Valladolid. At the Convent of San Bernardino de Siena, a 16th-century Spanish monastery built atop a cenote, the founders strived to create a self-sustaining community with sequestered vegetable gardens, an orchard and water below. I visited one afternoon for a look into the monastery’s watery depths, now capped with a grated well.

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Sacred Cenote near Chichén Itzá.Credit
Adriana Zehbrauskas for The New York Times

My most memorable cenote of the trip — the heavily visited Cenote Dzitnup — was 15 minutes by taxi from Valladolid’s central square. Two cenotes sit on the park’s property, the main one with lighted underground paths, steep stairways, side caverns and a vaulted sanctuary where a sunbeam cuts a pillar of light into an abysmal pool of clear, cold water.

I dived right in.

Maya culture long considered cenotes to be portals to the underworld, an expressway for offerings and sacrificed virgins sinking downward to the lap of a god. Jumping into Cenote Dzitnup — swimming in an underground lake, 100 feet below the jungle floor, free-diving deep underwater — I began to grasp the metaphysics of it all.

“It’s bottomless,” a local resident had said aboveground, referring to Dzitnup’s black pool. “Or at least they’ve never found the bottom.”

Swimming under a stalactite, its stony tip slightly submerged, I contemplated cave monsters and bottomless pits. Bats swooped along the ceiling high above.

The water below faded from clear to blue, then an inky black, the pillar of sunlight losing out to Dzitnup’s deepness. Light faded fast to dark at the doorway to the Maya underworld.

SNOOPING underground — or even underground and underwater — in the depths of a cenote is an approachable day-trip adventure for beachgoers in Cancún.

Or you could spend a lifetime exploring these water-filled sinkholes, which dot the flat jungle of the Yucatán by the thousands, hiding Maya ruins, sunken sacrificial offerings, submerged stalactites, eyeless fish and other wonders. Either way, a visit to at least one of these freshwater pools is highly recommended for any vacationer to the Yucatán Peninsula, where cenotes have nurtured human life for thousands of years.

For locals and tourists alike, swimming is the most popular way to explore a cenote, with cool spring water offering a retreat from the heat. Free-diving with snorkel gear down to about 20 is an excellent way to see these sinkholes.

A dozen or more parks with cenotes dot the Yucatán, most with inexpensive admission fees of less than $5. Cenote Dzitnup and Cenote Zací, both in Valladolid, fall in this category. Outside Playa del Carmen, Xcaret Eco Theme Park (52-984-871-5200; www.xcaret.com) has cenotes for swimming and an underground river that flows through the limestone bedrock. Park admission is $59.

For the scuba set, outfitters like Alltournative of Playa del Carmen (52-984-803-9999; www.alltournative.co) guide dives into cenotes and the caverns below throughout the eastern Yucatán. Hidden Worlds Cenote Park (52-984-877-8535; www.hiddenworlds.com.mx), near Tulum, has three daily scuba dive departures ($50 for a one-tank dive) and six daily snorkel tours, starting at $25. In Tulum, Cenote Dive Center (52-984-871-2232; www.cenotedive.com) offers guided snorkel trips to Gran Cenote, Casa Cenote and Dos Ojos Cenote for $45. The company’s scuba trips, which explore cenotes and underground caverns in the eastern Yucatán, start at $75 for a one-tank cavern trip.